[gmx-users] Re: Notes and warnings using grompp

Justin Lemkul jalemkul at vt.edu
Fri Sep 28 23:31:09 CEST 2012

On 9/28/12 5:13 PM, Sonia Aguilera wrote:
> Hi,
> I understand that usually it is needed to add counterions . I´m performing a
> free energy calculation and I want to see the free energy change without
> adding the ions. What I´m asking is why the program reads a total charge of
> -13.000002 not 13.0. The note says that it must be an integer, but I don´t
> know what to change or where. Should I ignore the note?

grompp reads a net charge of -13 because that's the charge (almost certainly) on 
the protein, per the parameters in the topology.  -13.000002 is close enough to 
an integer that the minor difference is due to rounding, as the link I provided 
before states.  Whether or not you ignore it depends on whether or not you think 
whatever you are modeling is reasonable.

> I have seen (second note) that since it is just a note, it can be ignored,
> but according with the parameters of the note, what do you think?

Notes are there to warn you that something is potentially wrong.  It looks like 
either your .mdp settings are inappropriate or you have a large charge group. 
This situation can lead to artifacts from incorrect neighbor searching or 
nonbonded calculations.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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